null Mon 24 Dec 07:33:55 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1zko-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1zko-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1zko-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1zko-4.0-parrot-noncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1zko-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1zko-4.0-parrot-noncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 07:33:59 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1zko-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1zko-4.0-parrot-noncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 165 and 0 Target number of residues in the AU: 165 Target solvent content: 0.6342 Checking the provided sequence file Detected sequence length: 136 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 272 Adjusted target solvent content: 0.40 Input MTZ file: 1zko-4.0-parrot-noncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 19 Cell parameters: 54.005 65.321 69.197 90.000 90.000 90.000 Input sequence file: 1zko-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 2176 target number of atoms Had to go as low as 0.70 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 47.500 4.001 Wilson plot Bfac: 68.38 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 2121 reflections ( 93.19 % complete ) and 0 restraints for refining 2401 atoms. Observations/parameters ratio is 0.22 ------------------------------------------------------ Starting model: R = 0.3777 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3424 (Rfree = 0.000) for 2401 atoms. Found 5 (11 requested) and removed 26 (5 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.52 4.03 Search for helices and strands: 0 residues in 0 chains, 2410 seeds are put forward NCS extension: 0 residues added, 2410 seeds are put forward Round 1: 27 peptides, 6 chains. Longest chain 6 peptides. Score 0.203 Round 2: 39 peptides, 8 chains. Longest chain 7 peptides. Score 0.238 Round 3: 40 peptides, 8 chains. Longest chain 7 peptides. Score 0.247 Round 4: 45 peptides, 9 chains. Longest chain 7 peptides. Score 0.253 Round 5: 58 peptides, 12 chains. Longest chain 7 peptides. Score 0.254 Taking the results from Round 5 Chains 12, Residues 46, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2121 reflections ( 93.19 % complete ) and 4637 restraints for refining 1927 atoms. 4465 conditional restraints added. Observations/parameters ratio is 0.28 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3297 (Rfree = 0.000) for 1927 atoms. Found 9 (9 requested) and removed 15 (4 requested) atoms. Cycle 2: After refmac, R = 0.3073 (Rfree = 0.000) for 1893 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 3: After refmac, R = 0.3245 (Rfree = 0.000) for 1872 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 4: After refmac, R = 0.2961 (Rfree = 0.000) for 1854 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 5: After refmac, R = 0.3199 (Rfree = 0.000) for 1837 atoms. Found 8 (8 requested) and removed 11 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.57 4.09 Search for helices and strands: 0 residues in 0 chains, 1868 seeds are put forward NCS extension: 0 residues added, 1868 seeds are put forward Round 1: 45 peptides, 11 chains. Longest chain 5 peptides. Score 0.176 Round 2: 56 peptides, 10 chains. Longest chain 10 peptides. Score 0.308 Round 3: 59 peptides, 11 chains. Longest chain 7 peptides. Score 0.297 Round 4: 64 peptides, 12 chains. Longest chain 8 peptides. Score 0.302 Round 5: 67 peptides, 12 chains. Longest chain 8 peptides. Score 0.325 Taking the results from Round 5 Chains 12, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2121 reflections ( 93.19 % complete ) and 3110 restraints for refining 1444 atoms. 2902 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2764 (Rfree = 0.000) for 1444 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 7: After refmac, R = 0.2905 (Rfree = 0.000) for 1424 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 8: After refmac, R = 0.2521 (Rfree = 0.000) for 1403 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 9: After refmac, R = 0.2786 (Rfree = 0.000) for 1396 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 10: After refmac, R = 0.2477 (Rfree = 0.000) for 1388 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.53 4.04 Search for helices and strands: 0 residues in 0 chains, 1434 seeds are put forward NCS extension: 0 residues added, 1434 seeds are put forward Round 1: 69 peptides, 16 chains. Longest chain 6 peptides. Score 0.208 Round 2: 88 peptides, 18 chains. Longest chain 9 peptides. Score 0.290 Round 3: 85 peptides, 16 chains. Longest chain 10 peptides. Score 0.330 Round 4: 81 peptides, 15 chains. Longest chain 8 peptides. Score 0.332 Round 5: 87 peptides, 14 chains. Longest chain 13 peptides. Score 0.404 Taking the results from Round 5 Chains 14, Residues 73, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2121 reflections ( 93.19 % complete ) and 3057 restraints for refining 1449 atoms. 2779 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2443 (Rfree = 0.000) for 1449 atoms. Found 6 (6 requested) and removed 30 (3 requested) atoms. Cycle 12: After refmac, R = 0.1957 (Rfree = 0.000) for 1410 atoms. Found 4 (6 requested) and removed 9 (3 requested) atoms. Cycle 13: After refmac, R = 0.1922 (Rfree = 0.000) for 1400 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 14: After refmac, R = 0.1890 (Rfree = 0.000) for 1401 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 15: After refmac, R = 0.2052 (Rfree = 0.000) for 1397 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.60 4.12 Search for helices and strands: 0 residues in 0 chains, 1446 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 1461 seeds are put forward Round 1: 61 peptides, 13 chains. Longest chain 7 peptides. Score 0.244 Round 2: 66 peptides, 13 chains. Longest chain 11 peptides. Score 0.284 Round 3: 75 peptides, 13 chains. Longest chain 11 peptides. Score 0.351 Round 4: 77 peptides, 14 chains. Longest chain 8 peptides. Score 0.334 Round 5: 77 peptides, 12 chains. Longest chain 14 peptides. Score 0.396 Taking the results from Round 5 Chains 12, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2121 reflections ( 93.19 % complete ) and 3112 restraints for refining 1456 atoms. 2864 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2819 (Rfree = 0.000) for 1456 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 17: After refmac, R = 0.2297 (Rfree = 0.000) for 1428 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 18: After refmac, R = 0.2020 (Rfree = 0.000) for 1416 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 19: After refmac, R = 0.1900 (Rfree = 0.000) for 1409 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 20: After refmac, R = 0.1840 (Rfree = 0.000) for 1409 atoms. Found 4 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.56 4.07 Search for helices and strands: 0 residues in 0 chains, 1450 seeds are put forward NCS extension: 0 residues added, 1450 seeds are put forward Round 1: 59 peptides, 13 chains. Longest chain 7 peptides. Score 0.228 Round 2: 85 peptides, 15 chains. Longest chain 11 peptides. Score 0.360 Round 3: 76 peptides, 14 chains. Longest chain 9 peptides. Score 0.327 Round 4: 81 peptides, 14 chains. Longest chain 11 peptides. Score 0.363 Round 5: 84 peptides, 14 chains. Longest chain 10 peptides. Score 0.383 Taking the results from Round 5 Chains 14, Residues 70, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2121 reflections ( 93.19 % complete ) and 3208 restraints for refining 1511 atoms. 2942 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2733 (Rfree = 0.000) for 1511 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. Cycle 22: After refmac, R = 0.2281 (Rfree = 0.000) for 1485 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 23: After refmac, R = 0.2213 (Rfree = 0.000) for 1472 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 24: After refmac, R = 0.2072 (Rfree = 0.000) for 1462 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. Cycle 25: After refmac, R = 0.2296 (Rfree = 0.000) for 1464 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.50 4.01 Search for helices and strands: 0 residues in 0 chains, 1507 seeds are put forward NCS extension: 0 residues added, 1507 seeds are put forward Round 1: 41 peptides, 10 chains. Longest chain 5 peptides. Score 0.177 Round 2: 67 peptides, 15 chains. Longest chain 6 peptides. Score 0.225 Round 3: 78 peptides, 16 chains. Longest chain 8 peptides. Score 0.278 Round 4: 83 peptides, 16 chains. Longest chain 7 peptides. Score 0.315 Round 5: 78 peptides, 15 chains. Longest chain 9 peptides. Score 0.310 Taking the results from Round 4 Chains 16, Residues 67, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2121 reflections ( 93.19 % complete ) and 3029 restraints for refining 1417 atoms. 2777 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2418 (Rfree = 0.000) for 1417 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. Cycle 27: After refmac, R = 0.1952 (Rfree = 0.000) for 1403 atoms. Found 4 (6 requested) and removed 9 (3 requested) atoms. Cycle 28: After refmac, R = 0.1858 (Rfree = 0.000) for 1396 atoms. Found 3 (6 requested) and removed 6 (3 requested) atoms. Cycle 29: After refmac, R = 0.2700 (Rfree = 0.000) for 1391 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 30: After refmac, R = 0.2003 (Rfree = 0.000) for 1376 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.52 4.03 Search for helices and strands: 0 residues in 0 chains, 1435 seeds are put forward NCS extension: 0 residues added, 1435 seeds are put forward Round 1: 65 peptides, 14 chains. Longest chain 7 peptides. Score 0.242 Round 2: 76 peptides, 14 chains. Longest chain 8 peptides. Score 0.327 Round 3: 68 peptides, 12 chains. Longest chain 8 peptides. Score 0.332 Round 4: 80 peptides, 16 chains. Longest chain 8 peptides. Score 0.293 Round 5: 74 peptides, 13 chains. Longest chain 9 peptides. Score 0.344 Taking the results from Round 5 Chains 13, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2121 reflections ( 93.19 % complete ) and 3259 restraints for refining 1476 atoms. 3028 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2155 (Rfree = 0.000) for 1476 atoms. Found 6 (7 requested) and removed 13 (3 requested) atoms. Cycle 32: After refmac, R = 0.1935 (Rfree = 0.000) for 1466 atoms. Found 5 (6 requested) and removed 10 (3 requested) atoms. Cycle 33: After refmac, R = 0.1883 (Rfree = 0.000) for 1456 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. Cycle 34: After refmac, R = 0.1704 (Rfree = 0.000) for 1451 atoms. Found 3 (6 requested) and removed 8 (3 requested) atoms. Cycle 35: After refmac, R = 0.1821 (Rfree = 0.000) for 1443 atoms. Found 2 (6 requested) and removed 13 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.53 4.04 Search for helices and strands: 0 residues in 0 chains, 1459 seeds are put forward NCS extension: 0 residues added, 1459 seeds are put forward Round 1: 65 peptides, 15 chains. Longest chain 6 peptides. Score 0.209 Round 2: 67 peptides, 15 chains. Longest chain 6 peptides. Score 0.225 Round 3: 68 peptides, 15 chains. Longest chain 6 peptides. Score 0.233 Round 4: 74 peptides, 16 chains. Longest chain 9 peptides. Score 0.248 Round 5: 75 peptides, 16 chains. Longest chain 6 peptides. Score 0.256 Taking the results from Round 5 Chains 16, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2121 reflections ( 93.19 % complete ) and 3400 restraints for refining 1522 atoms. 3180 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3126 (Rfree = 0.000) for 1522 atoms. Found 7 (7 requested) and removed 54 (3 requested) atoms. Cycle 37: After refmac, R = 0.2456 (Rfree = 0.000) for 1457 atoms. Found 3 (7 requested) and removed 15 (3 requested) atoms. Cycle 38: After refmac, R = 0.2573 (Rfree = 0.000) for 1428 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 39: After refmac, R = 0.2994 (Rfree = 0.000) for 1418 atoms. Found 6 (6 requested) and removed 24 (3 requested) atoms. Cycle 40: After refmac, R = 0.2802 (Rfree = 0.000) for 1389 atoms. Found 6 (6 requested) and removed 9 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.53 4.04 Search for helices and strands: 0 residues in 0 chains, 1420 seeds are put forward NCS extension: 0 residues added, 1420 seeds are put forward Round 1: 42 peptides, 10 chains. Longest chain 5 peptides. Score 0.186 Round 2: 54 peptides, 12 chains. Longest chain 5 peptides. Score 0.220 Round 3: 65 peptides, 13 chains. Longest chain 9 peptides. Score 0.276 Round 4: 68 peptides, 14 chains. Longest chain 9 peptides. Score 0.266 Round 5: 73 peptides, 14 chains. Longest chain 7 peptides. Score 0.305 Taking the results from Round 5 Chains 14, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2121 reflections ( 93.19 % complete ) and 2655 restraints for refining 1254 atoms. 2433 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3169 (Rfree = 0.000) for 1254 atoms. Found 5 (5 requested) and removed 12 (2 requested) atoms. Cycle 42: After refmac, R = 0.2803 (Rfree = 0.000) for 1233 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 43: After refmac, R = 0.2718 (Rfree = 0.000) for 1229 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 44: After refmac, R = 0.2894 (Rfree = 0.000) for 1226 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 45: After refmac, R = 0.2709 (Rfree = 0.000) for 1225 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.52 4.03 Search for helices and strands: 0 residues in 0 chains, 1272 seeds are put forward NCS extension: 0 residues added, 1272 seeds are put forward Round 1: 47 peptides, 11 chains. Longest chain 6 peptides. Score 0.195 Round 2: 57 peptides, 12 chains. Longest chain 9 peptides. Score 0.246 Round 3: 62 peptides, 13 chains. Longest chain 8 peptides. Score 0.252 Round 4: 62 peptides, 12 chains. Longest chain 11 peptides. Score 0.286 Round 5: 59 peptides, 12 chains. Longest chain 7 peptides. Score 0.262 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 1zko-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2121 reflections ( 93.19 % complete ) and 2438 restraints for refining 1189 atoms. 2250 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2715 (Rfree = 0.000) for 1189 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2478 (Rfree = 0.000) for 1178 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2448 (Rfree = 0.000) for 1175 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2357 (Rfree = 0.000) for 1172 atoms. Found 0 (5 requested) and removed 2 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 07:55:10 GMT 2018 Job finished. TimeTaking 21.25 Used memory is bytes: 21438600